methylMnM

jointly analyzing MeDIP-seq and MRE-seq data

Introduction

methyMnM was developed for jointly analyzing MeDIP-seq and MRE-seq data, which were derived from
methylated DNA immunoprecipitation (MeDIP) experiments [Weber et al., 2005] followed by
sequencing (MeDIP-seq) and methyl-sensitive restriction enzymes experiments for unmethylated
CpGs (MRE-seq). We have implemented the methylMnM method via a set of R functions with
the computational intensive parts written in C. The method consists three steps:

Data Pre-processing:

Calculate the CpG count of each window.

Calculate the MRE CpG count of each window.

Calculate MeDIP-seq tag count of each window of control and treatment samples.

Calculate MRE-seq tag count of each window of control and treatment samples.

Calculating p-values of each window by the methylMnM test.

FDR control.

We used a real dataset to illustrate the usage of the methylMnM package. The program performs best under any Linux system.

Installation

Before installing methylMnM package, the user have to install another two required R packages, which can be done
using the following commands.